check_maxP

Function to assess the distribution of maximum genotype probabilities (<code>maxP</code>), if these are available. The function
plots a violin graph showing the distribution of the samples' <code>maxP</code>.

Creation of linkage maps in polyploid species from marker dosage
scores of an F1 cross from two heterozygous parents. Currently works for outcrossing diploid, autotriploid, autotetraploid and autohexaploid species,
as well as segmental allotetraploids. Methods are described in a manuscript of Bourke et al. (2018) <doi:10.1093/bioinformatics/bty371>. Since version 1.1.0,
both discrete and probabilistic genotypes are acceptable input; for more details on the latter see Liao et al. (2021) <doi:10.1007/s00122-021-03834-x>.

Peter Bourke

polymapR

Linkage Analysis in Outcrossing Polyploids

Geert van Geest

Roeland Voorrips

Yanlin Liao

check_maxP function

<dl><dt>probgeno_df</dt>
<dd>A data frame as read from the scores file produced by function
<code>saveMarkerModels</code> of R package <code>fitPoly</code>, or alternatively, a data frame containing the following columns:<dl>
<dt>SampleName</dt>
<dd>Name of the sample (individual)</dd></dl></dd><dt>MarkerName</dt>
<dd>Name of the marker</dd><dt>P0</dt>
<dd>Probabilities of dosage score '0'</dd><dt>P1...</dt>
<dd>Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)</dd><dt>maxP</dt>
<dd>Maximum genotype probability identified for a particular individual and marker combination</dd><dt>maxgeno</dt>
<dd>Most probable dosage for a particular individual and marker combination</dd><dt>geno</dt>
<dd>Most probable dosage for a particular individual and marker combination, if <code>maxP</code> exceeds a user-defined threshold (e.g. 0.9), otherwise <code>NA</code></dd>
</dl>

Arguments

check your dataset's maxP distribution — check_maxP

<dl>

<dt>probgeno_df</dt>
<dd>A data frame as read from the scores file produced by function
<code>saveMarkerModels</code> of R package <code>fitPoly</code>, or alternatively, a data frame containing the following columns:<dl>
<dt>SampleName</dt>
<dd>Name of the sample (individual)</dd>

<dt>MarkerName</dt>
<dd>Name of the marker</dd>

<dt>P0</dt>
<dd>Probabilities of dosage score '0'</dd>

<dt>P1...</dt>
<dd>Probabilities of dosage score '1' etc. (up to max dosage, e.g. P4 for tetraploid population)</dd>

<dt>maxP</dt>
<dd>Maximum genotype probability identified for a particular individual and marker combination</dd>

<dt>maxgeno</dt>
<dd>Most probable dosage for a particular individual and marker combination</dd>

<dt>geno</dt>
<dd>Most probable dosage for a particular individual and marker combination, if <code>maxP</code> exceeds a user-defined threshold (e.g. 0.9), otherwise <code>NA</code></dd>


</dl></dd>

</dl>

check_maxP: check your dataset's maxP distribution

Description

Usage

Value

Arguments

Examples